1-209514837-G-A

Position:

• chr1-209514837-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.056 in 150,422 control chromosomes in the GnomAD database, including 502 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.056 (502 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0559 AC: 8407 AN: 150308 Hom.: 503 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0313

Gnomad ASJ AF: 0.00577

Gnomad EAS AF: 0.0588

Gnomad SAS AF: 0.0467

Gnomad FIN AF: 0.0171

Gnomad MID AF: 0.0446

Gnomad NFE AF: 0.0128

Gnomad OTH AF: 0.0486

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0560 AC: 8418 AN: 150422 Hom.: 502 Cov.: 32 AF XY: 0.0555 AC XY: 4068 AN XY: 73330

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.0313

Gnomad4 ASJ AF: 0.00577

Gnomad4 EAS AF: 0.0590

Gnomad4 SAS AF: 0.0466

Gnomad4 FIN AF: 0.0171

Gnomad4 NFE AF: 0.0128

Gnomad4 OTH AF: 0.0481

Alfa AF: 0.0394 Hom.: 47

Bravo AF: 0.0609

Asia WGS AF: 0.0590 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.69

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10489336; hg19: chr1-209688182;